Divergently coupled transcription or divergent transcription in which two neighboring promoters initiate transcription in opposite directions widely exists in many organisms from bacteria to humans. For instance, in murine and human cells, high throughput sequencing data showed that short noncoding RNAs (ncRNA) are always produced divergently from active promoters that direct transcription initiation of mRNA. Similarly, deep sequencing experiments and yeast whole genome tiling arrays demonstrated that a majority of yeast cryptic unstable transcripts (CUTs) are generated divergently from the promoter of functional genes.
Divergent transcription typically originates from two distinct promoters or transcription preinitiation complexes (PICs). These sense and upstream antisense transcripts arise from nucleosome depletion regions that contain two distinct hubs of transcription factor binding sites. In bacteria, many promoters are divergently coupled. For example, in the ilvYC operon of E. coli, the ilvY promoter is divergently coupled to the ilvC promoter. Transcriptional activities of the ilvY and ilvC promoters depend on the localized superhelical density around the promoter region. Another well-characterized example is the activation of S. typhimurium leu-500 promoter (Pleu-500) by divergently coupled transcription.